Hi Ross,

Am 13.01.2015 um 00:13 schrieb Ross:
> Hi  Björn,
> I'm a bit old fashioned and think I prefer a proper Galaxy tool rather than
> a notebook :) 


> So I've set up a temporary demonstration/test site of a
> toolfactory generated tool that does what I think I need - can some kind
> soul please test it and let me know how it goes ? If it's useful, it needs
> to be adjusted to depend on whatever version of package_R you want to work
> with - currently just uses the system R for demonstration purposes.
> I used the toolfactory2 (main toolshed) (which now allows any number of
> (optionally non editable) parameters!!!) to wrap the script shown at the
> bottom of https://wiki.galaxyproject.org/SetUpREnvironment. There are
> currently three parameters - the names of the R/BioC packages from
> sessionInfo(), the local directory where all the tarballs should be stowed
> and the XML output prefix to prepend to each row of the generated XML
> stanza for tool_dependencies.xml
> The resulting toolshed tarball was uploaded to a local toolshed and then
> installed to produce a new tool in the "tool generators" section
> - r_bioc_depgen Generate dependencies for R/BioC packages
> If you import the history at
> you will see the toolfactory job (#1,#2,#3) - rerunning will show how the
> parameters are defined - fugly but it does work.
> After generating/uploading/installing the new tool, outputs from a test run
> are in #4 and #5 for DESeq

This is cool!
I have to try this on a few packages!
This could also be of interest for our GSOC idea:

Thanks Ross for working on this!

> Comments and suggestions welcomed!
> On Sun, Jan 11, 2015 at 10:41 PM, Björn Grüning <bjoern.gruen...@gmail.com>
> wrote:
>> Hi Ross,
>> you are absolutely right.
>> My download_store repository is exactly for this purpose.
>> https://github.com/bgruening/download_store
>> If you are interested we could integrate your additional magic into the
>> notebook.
>> Thanks,
>> Bjoern
>> Am 11.01.2015 um 01:33 schrieb Ross:
>>> Hi, Björn,
>>> Looks pretty similar!
>>> Aren't the links your notebook generates transient? I think if you put
>> them
>>> into a tool_dependencies.xml, they will fail permanently immediately
>> after
>>> any of the package authors updates one of the relevant svn repositories?
>>> AFAIK, it looks like the whole BioC/CRAN infrastructure is automated so a
>>> link that works today like
>>> http://cran.fhcrc.org/src/contrib/Rcpp_0.11.3.tar.gz will fail when Rcpp
>>> next gets updated and Rcpp_0.11.3.tar.gz is migrated to
>>> http://cran.fhcrc.org/src/contrib/00Archive/Rcpp/ with a replacement
>> (eg)
>>> http://cran.fhcrc.org/src/contrib/Rcpp_0.11.4.tar.gz appearing in the
>>> contrib directory?
>>> That's why my more complex script downloads all the latest archives into
>> my
>>> local github archive repo and generates a permanent link to suit that
>>> github repo.
>>> We definitely need an automated solution as this is a really infuriating
>>> aspect of trying to make code relying on R/BioC packages reproducible.
>>> On Thu, Jan 8, 2015 at 11:28 PM, Björn Grüning <
>> bjoern.gruen...@gmail.com>
>>> wrote:
>>>> Hi Ross,
>>>> this is great!
>>>> Have you seen this notebook?
>> http://nbviewer.ipython.org/github/bgruening/notebooks/blob/master/R/extract_all_dependencies_from_an_r_package.ipynb
>>>> It tries to do the same thing. Maybe it's also worth to mention? Maybe
>>>> we can enhance it?
>>>> Thanks,
>>>> Bjoern
>>>> Am 08.01.2015 um 08:09 schrieb Ross:
>>>>> This may be helpful for anyone else struggling to get complex nested R
>>>>> package dependency installation from the tool shed sorted out. That
>> whole
>>>>> can of worms. While we have setup_r_packages, the developer still has
>> to
>>>>> figure out the right magical incantation and make sure the tarballs are
>>>>> available.
>>>>> https://wiki.galaxyproject.org/SetUpREnvironment has some notes I've
>>>>> started - contribitions welcome.
>>>>> It has a more or less reusable R script to generate
>> tool_dependencies.xml
>>>>> boilerplate, assuming you set the constant libdir to your local git
>>>>> repository path where those tarballs will be downloaded from.
>>>>> I hope this helps someone!
>>>>> Could make a tool to do this if enough developers want access to it
>>>> without
>>>>> the pain of managing yet another R script?
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